| Tool | Type | PMID | Journal | Year | Description |
|---|---|---|---|---|---|
| LTRHarvest | LTR | 18194517 | BMC Bioinformatics | 2008 | An efficient and flexible software for de novo detection of LTR retrotransposons |
| LTRdigest | LTR | 19786494 | Nucleic Acids Res | 2009 | A novel software tool for automated annotation of internal features of putative LTR retrotransposons |
| RetroTector | LTR/ERV | 19534753 | BMC Bioinformatics | 2009 | A rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences |
| SINE-Finder | SINE | 21908723 | Plant Cell | 2011 | A tool for the targeted discovery of tRNA-derived SINEs |
| LTRsift | LTR | 23131050 | Mob DNA | 2012 | A graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons |
| MGEScan | LTR/LINE | 27153595 | Bioinformatics | 2016 | A Galaxy-based system for identifying retrotransposons in genomes |
| SINE_scan | SINE | 28062442 | Bioinformatics | 2017 | An efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets |
| LTR_retriever | LTR | 29233850 | Plant Physiol | 2018 | A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons |
| TE-Learner | LTR | 29684010 | PLoS Comput Biol | 2018 | A machine learning based framework to identify and classify long terminal repeat retrotransposons |
| LtrDetector | LTR | 31159720 | BMC Genomics | 2019 | A tool-suite for detecting long terminal repeat retrotransposons de-novo |
| AnnoSINE | SINE | 34792587 | Plant Physiol | 2022 | A short interspersed nuclear elements annotation tool for plant genomes |
| Inpactor2 | LTR | 36502372 | Brief Bioinform | 2023 | A software based on deep learning to identify and classify LTR-retrotransposons in plant genomes |
| MegaLTR | LTR | 37810401 | Front Plant Sci | 2023 | A web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes |
| DANTE and DANTE_LTR | LTR | 39211332 | NAR Genom Bioinform | 2024 | Lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes |
| Look4LTRs | LTR | 38627766 | Mob DNA | 2024 | A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats |
| RetroSeq | TE | 23233656 | Bioinformatics | 2013 | Transposable element discovery from next-generation sequencing data |
| TEMP | TE | 24753423 | Nucleic Acids Res | 2014 | A computational method for analyzing transposable element polymorphism in populations |
| Mobster | TE | 25348035 | Genome Biol | 2014 | Accurate detection of mobile element insertions in next generation sequencing data |
| Tangram | TE | 25228379 | BMC Genomics | 2014 | A comprehensive toolbox for mobile element insertion detection |
| ITIS | TE | 25887332 | BMC Bioinformatics | 2015 | A bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data |
| MELT | TE | 28855259 | Genome Res | 2017 | "A software package, written in Java, that discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data" |
| TIP_finder | TE | 32917036 | Biology (Basel) | 2020 | An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets |
| T-lex3 | TE | 31580402 | Bioinformatics | 2020 | An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data |
| HiTea | TE | 33136153 | Bioinformatics | 2021 | A computational pipeline to identify non-reference transposable element insertions in Hi-C data |
